Epigenetic Histone Landscape Profiles in HIV

PROJECT SUMMARY/ABSTRACT The overarching goal of this R21 proposal is to test the hypothesis that DNA vaccines induce durable innate memory in HIV-infected humans by characterizing the evolution of the epigenetic and transcriptional landscape in subjects who have been immunized using a novel HIV DNA vaccine. We recently used a "systems immunology" approach to successfully map the epigenomic and transcriptional landscape of immunity to influenza vaccination in healthy humans. Vaccination against seasonal influenza, with or without AS03 adjuvant, resulted in persistently reduced expression of H3K27ac in monocytes and myeloid dendritic cells (mDCs), which was associated with impaired cytokine responses to toll like receptor (TLR) stimulation. Single cell analysis revealed an epigenomically-distinct subcluster of myeloid cells with reduced chromatin accessibility at activator protein-1 (AP-1) targeted loci after vaccination, persistently increased chromatin accessibility at loci targeted by interferon (IFN) response factors (IRFs), which was associated with elevated expression of antiviral genes, type 1 IFN production, and heightened resistance to infection with the heterologous viruses Zika and dengue. In another recent paper, we have shown that the Pfizer-BioNTech mRNA prime-boost vaccine (BNT162b2) resulted in enhanced innate immune responses, evidenced by a greater frequency of CD14+CD16+ inflammatory monocytes, higher plasma IFN-γ, and a transcriptional signature of innate antiviral immunity. We will replicate this "systems immunology" framework to characterize innate memory using peripheral blood mononuclear cells (PBMCs) from HIV+ subjects in the A5369 prime-boost DNA vaccine trial (NCT03560258). Induction and durability of innate memory will be studied across 3 aims in this R21. Aim 1 will identify histone posttranslational modifications (HPTMs) in PBMCs at single-cell resolution using Epigenetic Landscape Profiling using Cytometry by Time Of Flight (EpiTOF). We will test the hypothesis that antigen-specific DNA vaccination induces innate memory through epigenetic reprogramming, expands with each sequential prime and boost (week 0 < week 6 << week 26), and is preserved at week 48. Aim 2 will identify gene transcript modules, and their evolution over time, associated with innate memory. We will test the hypothesis that antigen-specific DNA vaccination induces durable innate memory through transcriptomic changes and expands with each sequential prime and boost (week 0 << week 26 > week 48). We will test the hypothesis that transcriptional modules that characterize innate memory in influenza and SARS-CoV-2 vaccination are generalizable to HIV DNA vaccines. We also expect to identify unique subsets of cells, transcripts, and pathways associated with innate memory that differ from influenza and SARS-CoV-2. Aim 3 will perform systems immunology analysis by integrating EpiTOF and transcriptomic data from Aims 1 &2, and comparing with similar data from influenza and SARS-CoV-2 vaccinated subjects testing the hypothesis that there are generalizable mechanisms underlying innate memory across vaccine platforms, and cells and pathways specific to DNA vaccines and/or HIV infection.